Tiles issues with multiple layers

in General
After you draw on a tile, is it possible to assign it to a tile (like make an unmapped tile tile 0 without copy/pasting). Does the layer features just not work with tiles or am I just missing something? It is rough doing animation without this feature (or just not knowing how to do it if it is enabled).
Comments
The tile system is not connected with multiple layers, only the selected layer, so if you have a character with multiple layers for ie. arms, head, feet etc.. then you have to copy the information from each layer and apply it to the next tile. Alternatively you can make duplicates of your layers and use the "Apply to next down" that will merge your layers together but keep the tile mapping. I know it's a rather tedious process but there's no other solution currently except than what you're already doing.